MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
First, forget about lord thorgal :D
Second, as I already told you your questions are perfectly ok. They are going to the right spot.
Third, Cartesian XYZ on 3D printers is done the typical way, X+ is going to the right, Y+ is going from you and Z+ is going up. When looking at ToyREP from the side of Y-motor (having ramps in the back) than both X and Y axis are homed in max in distant right corner. Than when homed and size limits are set, the only way printer will allow you to go is X- and Y- until you hit 0,0 coordinate in the closest left corner. Than the motors will stop and will let you go only X + and Y+ until you almost hit endstops again.
If the motors are working but in wrong direction, there are two ways to change to the direction. One mechanical as you suggested is to turn the connector and second software to change the line in configuration.h => define INVERT_Y_DIR to false or true (false is recommended, if the connector is installed the same way as on other motors).